From 2009.igem.org
/*
Copyright: synbiowave
License: GPL
Authors: Jörg Walossek
Version: 0.1
DESCRIPTION:
This class provides the static methods used in the file up- and download.
*/
package org.synbiowave.biojava;
import java.io.BufferedInputStream;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import org.biojava.bio.BioException;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.ProteinTools;
import org.biojava.bio.seq.RNATools;
import org.biojavax.Namespace;
import org.biojavax.RichObjectFactory;
import org.biojavax.bio.seq.RichSequence;
import org.biojavax.bio.seq.RichSequenceIterator;
import org.synbiowave.database.Sequence;
// TODO: Auto-generated Javadoc
/**
* The Class Util.
*/
public class Util {
/** The Constant ns. */
private static final Namespace ns=RichObjectFactory.getDefaultNamespace();
/**
* Instantiates a new util.
*/
public Util() {}
/**
* Read.
*
* @param in the in
*
* @return the rich sequence iterator
*
* @throws ClassNotFoundException the class not found exception
* @throws IOException Signals that an I/O exception has occurred.
*/
public static RichSequenceIterator read(InputStream in) throws ClassNotFoundException,IOException{
RichSequence.IOTools.registerFormat(org.biojavax.bio.seq.io.FastaFormat.class);
RichSequence.IOTools.registerFormat(org.biojavax.bio.seq.io.EMBLFormat.class);
RichSequence.IOTools.registerFormat(org.biojavax.bio.seq.io.EMBLxmlFormat.class);
RichSequence.IOTools.registerFormat(org.biojavax.bio.seq.io.GenbankFormat.class);
RichSequence.IOTools.registerFormat(org.biojavax.bio.seq.io.INSDseqFormat.class);
return RichSequence.IOTools.readStream(new BufferedInputStream(in),ns);}
/**
* Write.
*
* @param out the out
* @param sequences the sequences
* @param format the format
*
* @throws IOException Signals that an I/O exception has occurred.
*/
public static void write(OutputStream out,RichSequenceIterator sequences,String format) throws IOException{
if(format.equalsIgnoreCase("fasta")){
RichSequence.IOTools.writeFasta(out,sequences,ns);}
else if(format.equalsIgnoreCase("embl")){
RichSequence.IOTools.writeEMBL(out,sequences,ns);}
else if(format.equalsIgnoreCase("genbank")){
RichSequence.IOTools.writeGenbank(out,sequences,ns);}}
/**
* Convert to rich sequence.
*
* @param sequence the sequence
*
* @return the org.biojava.bio.seq. sequence
*
* @throws BioException the bio exception
* @throws ClassNotFoundException the class not found exception
* @throws IOException Signals that an I/O exception has occurred.
*/
public static org.biojava.bio.seq.Sequence convertToRichSequence(Sequence sequence) throws
BioException,ClassNotFoundException,IOException{
org.biojava.bio.seq.Sequence s=null;
if(sequence.getPlain()!=null){s=Util.read(new ByteArrayInputStream(sequence.getPlain().getBytes())).nextSequence();}
else{
if(sequence.getType().equals("DNA")){s=DNATools.createDNASequence(sequence.getSequence(),sequence.getName());}
else if(sequence.getType().equals("RNA")){
s=RNATools.createRNASequence(sequence.getSequence(),sequence.getName());}
else{s=ProteinTools.createProteinSequence(sequence.getSequence(),sequence.getName());}}
// StrandedFeature.Template temp = new StrandedFeature.Template();
// temp.annotation = org.biojava.bio.Annotation.EMPTY_ANNOTATION;
// temp.location = new RangeLocation(10,25);
// temp.source = "";
// temp.strand = StrandedFeature.POSITIVE;
// temp.type = "";
//
// Feature f = s.createFeature(temp);
// temp = (StrandedFeature.Template)f.makeTemplate();
// temp.location = new RangeLocation(30,35);
// temp.strand = StrandedFeature.NEGATIVE;
// s.createFeature(temp);
// }
// rs=Tools.createRichSequence(sequence.getName(),sequence.getSequence(),AlphabetManager.alphabetForName(sequence.getType()));
// rs.setDescription(sequence.getName());}
// ArrayList<Annotation> annotations=sequence.getAnnotations();
// Set<Feature> features=new HashSet<Feature>();
// for(Annotation a:annotations){
// if(a.getName().equals("feature")){
// Feature f=RichFeature.Tools.makeEmptyFeature();
// f.setType(a.getValue());
// f.setLocation(LocationTools.makeLocation(a.getRange().getStart(),a.getRange().getEnd()));
// features.add(f);}}}
return s;}
}
"
